HDF5 version 1.8.5 released on Fri Jun 4 13:27:31 CDT 2010
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.4 and HDF5 1.8.5, and
contains information on the platforms tested and known problems in HDF5-1.8.5.
For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt
in the release_docs/ directory of the HDF5 source.
Links to the HDF5 1.8.5 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.5 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.5 can be accessed directly at this location:
http://www.hdfgroup.org/HDF5/doc/
New features in the HDF5-1.8.x release series, including brief general
descriptions of some new and modified APIs, are described in the "What's New
in 1.8.0?" document:
http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
All new and modified APIs are listed in detail in the "HDF5 Software Changes
from Release to Release" document, in the section "Release 1.8.5 (current
release) versus Release 1.8.4":
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
========
- New Features
- Support for New Platforms, Languages, and Compilers
- Bug Fixes since HDF5-1.8.4
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- CMake Early Access: This release adds support for building HDF5 using
the CMake system. Initial work has targeted Windows, but other platforms
can be used. See the CMake.TXT file for more information. Version
2.8.1 of CMake is required.
- Configure now adds appropriate defines for supporting large (64-bit)
files on all systems, where supported, by default, instead of only Linux.
This large file support is controllable with the --enable-largefile
configure option. The Linux-specific --enable-linux-lfs option has been
deprecated in favor of this new option. Please note that specifying
--disable-large does NOT attempt to "turn off" largefile support if it
is natively supported by the compiler, but rather just disables
configure from actively trying to add any additional compiler flags.
(MAM - 2010/05/05 - Bug # 1772/1434)
- Fixed an signal handling mask error in H5detect that might result in
SIGBUS or SIGSEGV failures in some platforms such as Linux on Sparc.
(AKC - 2010/4/28 - Bug # 1764)
- Fixed various "strict aliasing" problems, allowing higher levels
of compiler optimization (in particular, allowing '-O3' to work
with recent versions of GCC). (QAK - 2010/04/26)
- Upgraded versions of autotools used to generate configuration suite.
We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b.
(MAM - 2010/04/15)
- Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM
compilers so that the IBM compiler options can be added properly. This
allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be
recognized. (AKC - 2009/11/26)
Library
-------
- Performance is substantially improved when extending a dataset with early
allocation. (NAF - 2010/03/24 - Bug # 1637)
- Added support for filtering densely stored groups. Many of the API
functions related to filters have been extended to support dense groups
as well as datasets. Pipeline messages can now be stored in a group's
object header. (NAF/QAK - 2009/11/3)
Parallel Library
----------------
- None
Tools
-----
- h5dump: Added the new packed bits feature which prints packed bits stored
in an integer dataset. (AKC/ADB - 2010/5/7)
- h5diff: Fixed incorrect behavior (hang) in parallel mode when specifying
invalid options (ex: -v and -q). (JKM - 2010/02/17)
- h5diff: Added new flag --no-dangling-links (see --help for details).
(JKM - 2010/02/10)
- h5diff: Added new flag --follow-symlinks (see --help for details).
(JKM - 2010/01/25)
- h5diff: Added a fix to correct the display of garbage values when
displaying big-endian data on a little-endian machine. (JKM - 2009/11/20)
High-Level APIs
---------------
- None
F90 API
-------
- None
C++ API
-------
- New member functions
+ Overloaded CommonFG::getObjnameByIdx to take char* for name.
+ Overloaded CommonFG::getObjTypeByIdx to return type name as a char*.
(BMR - 2010/05/10)
+ Added DataSet::getInMemDataSize() to simplify getting the dataset's
data size in memory. (BMR - 2009/07/26)
Support for New Platforms, Languages, and Compilers
===================================================
- AIX 6.1 has been added. (AKC - 2010/1/4)
Bug Fixes since HDF5-1.8.4
==========================
Configuration
-------------
- Fixed various "strict aliasing" problems, allowing higher levels
of compiler optimization (in particular, allowing '-O3' to work
with recent versions of GCC). (QAK - 2010/04/26)
Library
-------
- Fixed a file corruption bug that could happen when shrinking a compressed
dataset. (NAF - 2010/05/20)
- Fixed some memory leaks in VL datatype conversion when strings are
used as fill values. (MAM - 2010/05/12 - Bug # 1826)
- Fixed an H5Rcreate failure when passing in a -1 for the dataspace
identifier. (ADB - 2010/4/28)
- Fixed a bug when copying objects with NULL references with the
H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - Bug # 1815)
- Added a mechanism to the H5I interface to save returned object identifier
structures for immediate re-use if needed. This addresses a potential
performance issue by delaying the case when the next identifier to be
registered has grown so large that it wraps around and needs to be
checked to see whether it is available for distribution.
(MAM - 2010/03/15 - Bug # 1730)
- Files can now be concurrently opened more than once using the core file
driver, as long as the backing store is used. (NAF - 2010/03/09)
- Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External
links will now be expanded if this flag is set.
(NAF - 2010/03/05 - Bug # 1733)
- Fixed a bug where the library, when traversing an external link, would
reopen the source file if nothing else worked. (NAF - 2010/03/05)
- Fixed a bug where fractal heap identifiers for attributes and shared
object header messages could be incorrectly encoded in the file for
files created on big-endian platforms.
Please see http://www.hdfgroup.org/HDF5/release/known_problems if you
suspect you have a file with this problem.
(QAK - 2010/02/23 - Bug # 1755)
- Fixed an intermittent bug in the b-tree code which could be triggered
by expanding and shrinking chunked datasets in certain ways.
(NAF - 2010/02/16)
- H5Tdetect_class said a VL string is a string type. But when it's in
a compound type, it said it's a VL type. THis has been fixed to be
consistent; it now always returns a string type.
(SLU - 2009/12/10 - Bug # 1584)
- Allow "child" files from external links to be correctly located when
relative to a "parent" file that is opened through a symbolic link.
(QAK - 2009/12/01)
Parallel Library
----------------
- Parallel mode in AIX will fail some of the testcheck_version.sh tests
where it treats "exit(134) the same as if process 0 had received an abort
signal. Fixed. (AKC - 2009/11/3)
Tools
-----
- Fixed h5ls to return exit code 1 (error) when a non-existent file is
specified. (JKM - 2010/04/27 - Bug # 1793)
- Fixed h5copy failure when copying a dangling link that is specified
directly. (JKM - 2010/04/22 - Bug # 1817)
- Fixed an h5repack failure that lost attributes from a dataset of
reference type. (JKM - 2010/3/25 - Bug # 1726)
- Fixed h5repack error that set NULL for object reference values for
datasets, groups, or named datatypes. (JKM - 2010/03/19 - Bug # 1814)
F90 API
------
- None
C++ API
------
- The constructor PropList::PropList(id) was fixed to act properly
according to the nature of 'id'. When 'id' is a property class
identifier, a new property list will be created. When 'id' is a
property list identifier, a copy of the property list will be made.
(BMR - 2010/5/9)
- The parameters 'size' and 'bufsize' in CommonFG::getLinkval and
CommonFG::getComment, respectively, now have default values for the
user's convenience. (BMR - 2009/10/23)
- NULL pointer accessing was fixed. (BMR - 2009/10/05 - Bug # 1061)
- Read/write methods of DataSet and Attribute classes were fixed
to handle string correctly. (BMR - 2009/07/26)
High-Level APIs:
------
- Fixed a bug in H5DSattach_scale, H5DSis_attached, and H5DSdetach_scale
caused by using the H5Tget_native_type function to determine the native
type for reading the REFERENCE_LIST attribute. This bug was exposed
on Mac PPC. (EIP - 2010/05/22 - Bug # 1851)
- Fixed a bug in the H5DSdetach_scale function when 0 bytes were
allocated after the last reference to a dimension scale was removed
from the list of references in a VL element of the DIMENSION_LIST
attribute. Modified the function to comply with the specification:
the DIMENSION_LIST attribute is now deleted when no dimension scales
are left attached. (EIP - 2010/05/14 - Bug # 1822)
Fortran High-Level APIs:
------
- None
Platforms Tested
================
The following platforms and compilers have been tested for this release.
AIX 5.3 xlc 7.0.0.9, 8.0.0.20, 9.0.0.4
(LLNL Up) xlC 7.0.0.9, 8.0.0.20, 9.0.0.4
xlf 9.1.0.9, 10.1.0.9, 11.1.0.7
mpcc_r 7.0.0.9
mpxlf_r 09.01.0000.0008
AIX 6.1 xlc 10.1.0.6
(NCSA BP) xlC 10.1.0.6
xlf 12.1.0.7
Cray XT3 (2.1.56) cc (pgcc) 10.0-0
(SNL red storm) ftn (pgf90) 10.0-0
CC (pgCC) 10.0-0
FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
(duty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.3.4 20090419
g++ 4.3.4 20090419
gfortran 4.3.4 20090419
FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
(liberty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.4.1 20090421
g++ 4.4.1 20090421
gfortran 4.4.1 20090421
Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 20080704 and 4.4.2
#1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2
(jam) g++ (GCC) 4.1.2 20080704 and 4.4.2
G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
Absoft 32-bit Fortran 95 10.0.7
PGI C, Fortran, C++ 10.4-0 32-bit
Intel(R) C, C++, Fortran Compilers for 32-bit
applications, Version 11.1 Build 20090827
MPICH mpich2-1.0.8 compiled with
gcc 4.1.2 and GNU Fortran (GCC) 4.1.2
Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 and gcc 4.4.2
x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2
(amani) g++ (GCC) 4.1.2 20080704 and 4.4.2
G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
Intel(R) C, C++, Fortran Compilers for
applications running on Intel(R) 64,
Version 11.1 Build 20090827.
PGI C, Fortran, C++ Version 10.4-0
for 32 & 64-bit target on x86-64
MPICH mpich2-1.0.8 compiled with
gcc 4.1.2 and GNU Fortran (GCC) 4.1.2
Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 11.0.074
SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 11.0.074
(cobalt) SGI MPI 1.38
SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-14
(linew) Sun Fortran 95 8.3 SunOS_sparc
Patch 127000-13
Sun C++ 5.9 SunOS_sparc Patch 124863-23
Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026
92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026
perfctr #7 SMP Open MPI 1.2.2
(abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
compiled with icc v10.0.026 and ifort 10.0.026
Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
SMP x86_64 GNU/Linux applications running on Intel(R) 64,
(SNL Glory) Versions 11.1.
Windows XP Visual Studio 2008 w/ Intel Fortran 10.1
Cygwin(1.7.5 native gcc(4.3.4) compiler and
gfortran)
Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1
Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1
Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1
MAC OS 10.6.3 (Intel) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1
(pahra) GNU Fortran (GCC) 4.5.0 20090910
i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1
Intel C, C++ and Fortran compilers 11.1
MAC OS 10.5.8 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
(tejeda)
MAC OS 10.5 (PPC) powerpc-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
(juniper-w)
OpenVMS Alpha V8.3 HP C V7.3-009
HP C++ V7.3-009
HP Fortran V8.0-1-104669-48GBT
Supported Configuration Features Summary
========================================
In the tables below
y = tested and supported
n = not supported or not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
Platform C F90 F90 C++ zlib SZIP
parallel parallel
Solaris2.10 32-bit n y n y y y
Solaris2.10 64-bit n y n y y y
Windows XP n y(4) n(4) y y y
Windows XP x64 n y(4) n(4) y y y
Windows Vista n y(4) n(4) y y y
Windows Vista x64 n y(4) n(4) y y y
Mac OS X 10.5 PPC n n n n y n
Mac OS X 10.5 Intel n y n y y y
Mac OS X 10.6 Intel n y n y y y
AIX 5.3 32- and 64-bit n y n y y n
AIX 6.1 32- and 64-bit n y n y y n
FreeBSD 6.3-STABLE 32&64 bit n y n y y y
RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y
RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y
RedHat EL5 2.6.18-128 i686 Intel W n y n y y n
RedHat EL5 2.6.18-128 i686 PGI W n y n y y n
SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
SuSe Linux 2.6.16 x86_64 Intel W n y n y y n
SuSe Linux 2.6.16 x86_64 PGI W n y n y y y
SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y
RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
Cray XT3 2.1.56 y y y y y n
OpenVMS Alpha V8.3 n y n y y n
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Solaris2.10 32-bit y y y y
Solaris2.10 64-bit y y y y
Windows XP y y(4) y n
Windows XP x64 y y(4) y n
Windows Vista y y(4) y n
Windows Vista x64 y y(4) y n
Mac OS X 10.5 PPC y n n n
Mac OS X 10.5 (Intel) y(5) n y n
Mac OS X 10.6 (Intel) y(5) n y n
AIX 5.3 32- and 64-bit n n n n
AIX 6.1 32- and 64-bit n n n n
FreeBSD 6.3-STABLE 32&64 bit y n y y
RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y
RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y
RedHat EL5 2.6.18-128 i686 Intel W y y y n
RedHat EL5 2.6.18-128 i686 PGI W y y y n
SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y
SuSe Linux 2.6.16 x86_64 Intel W y y y n
SuSe Linux 2.6.16 x86_64 PGI W y y y n
SuSe Linux 2.6.16 SGI Altix ia64 C y n
RedHat EL4 2.6.18 Xeon Lustre C y y y n
Cray XT3 2.1.56 n n n n
OpenVMS Alpha V8.3 n n n n
(1) Fortran compiled with g95.
(2) With PGI and Absoft compilers.
(3) With PGI compiler for Fortran.
(4) Using Visual Studio 2008. (Cygwin shared libraries are not
supported.)
(5) Shared C and C++ are disabled when Fortran is configured in.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* The library's test dt_arith.c exposed a compiler's rounding problem on
Cygwin when converting from unsigned long long to long double. The
library's own conversion works correctly. A macro is defined for Cygwin
to skip this test until we can solve the problem. (Please see bug #1813.)
SLU - 2010/5/5
* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
structure H5FD_class_t changed in 1.8. There is a new parameter added to
get_eoa and set_eoa callback functions. A new callback function
get_type_map was added. The public function H5FDrealloc was taken
out in 1.8. The problem only happens when users define their own driver
for 1.6 and try to plug it into a 1.8 library. This affects a very small
number of users. (See bug report #1279.) SLU - 2010/2/2
* MinGW has a missing libstdc++.dll.a library file and will not successfully
link C++ applications/tests. Do not use the enable-cxx configure option.
Read all of the INSTALL_MINGW.txt file for all restrictions.
ADB - 2009/11/11
* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used.
The error is due to insufficient memory requested. Request a large amount
of runtime memory by setting the following environment variable for more
memory.
LDR_CNTRL=MAXDATA=0x20000000@DSA
AKC - 2009/10/31
* The PathScale MPI implementation, accessing a Panasas file system, would
cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not
existing. This is due to the MPI_File_open() call failing if the amode has
the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
* Parallel tests failed with 16 processes with data inconsistency at testphdf5
/ dataset_readAll. Parallel tests also failed with 32 and 64 processes with
collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
with MPI IO. CMC - 2009/04/28
* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c
would fail to compile. Actually bad H5Tinit.c is produced. If -O (same
as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail.
When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all
tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc.
AKC - 2009/04/20
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
are expected to fail and should exit with a non-zero code but the yod
command does not propagate the exit code of the executables. Yod always
returns 0 if it can launch the executable. The test suite shell expects
a non-zero for this particular test, therefore it concludes the test has
failed when it receives 0 from yod. Skip all the "failing" test for now
by changing them as following.
======== Original tools/h5ls/testh5ls.sh =========
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== Change to ===============================
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
==================================================
======== Original tools/h5copy/testh5copy.sh =========
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
H5LSTEST $FILEOUT
======== Change to ===============================
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
echo SKIP H5LSTEST $FILEOUT
==================================================
AKC - 2008/11/10
* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
message, "yod allocation delayed for node recovery". This interferes with
test suites that do not expect seeing this message. See the section of "Red
Storm" in file INSTALL_parallel for a way to deal with this problem.
AKC - 2008/05/28
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
use -mp -O1 compilation flags to build the libraries. A higher level of
optimization causes failures in several HDF5 library tests.
* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
the application asks to do collective IO, we have found that when using 4
processors, a simple collective write will sometimes be hung. This can be
verified with t_mpi test under testpar.
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
There was a bug in the calculation of the Fletcher32 checksum in the
library before v1.6.3; the checksum value was not consistent between big-
endian and little-endian systems. This bug was fixed in Release 1.6.3.
However, after fixing the bug, the checksum value was no longer the same as
before on little-endian system. Library releases after 1.6.4 can still read
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
SLU - 2005/6/30
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
messages like "INFO: 0031-XXX ...". This is from the command `poe'.
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
and run the tests again.
The tests may fail with messages like "The socket name is already in use,"
but HDF5 does not use sockets. This failure is due to problems with the
poe command trying to set up the debug socket. To resolve this problem,
check to see whether there are many old /tmp/s.pedb.* files staying around.
These are sockets used by the poe command and left behind due to failed
commands. First, ask your system administrator to clean them out.
Lastly, request IBM to provide a means to run poe without the debug socket.
* The --enable-static-exec configure flag will only statically link libraries
if the static version of that library is present. If only the shared version
of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
for example, only have shared versions), the flag should still result in a
successful compilation, but note that the installed executables will not be
fully static. Thus, the only guarantee on these systems is that the
executable is statically linked with just the HDF5 library.
* There is also a configure error on Altix machines that incorrectly reports
when a version of Szip without an encoder is being used.
* On FREE-BSD systems when shared libraries are disabled, make install fails
in install-examples with the error '"Makefile", line 635: Need an operator'.
When this error occurs removing or commenting out the line "export
LD_LIBRARY_PATH=$(LL_PATH)" (line 635 in examples/Makefile) will allow make
install to finish installing examples. The problem will be fixed in the
next release. LRK - 2010/05/26
* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which
is the default on that system) does not work properly and results in
failures during make check (in a static build) and make installcheck (during
a shared build). This appears to be a compiler optimization problem.
Reducing optimization by setting CFLAGS to -O1 or below resolves the issue.
Alternatively, using a newer version of the compiler (11.0) also works as
intended. MAM - 2010/06/01
